Package: occumb 1.3.0

occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

Fits community site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>, Fukaya and Hasebe (2025) <doi:10.1002/1438-390X.12219>.

Authors:Keiichi Fukaya [aut, cre], Ken Kellner [cph], Mika Takahashi [aut], Martyn Plummer [ctb], Koji Makiyama [ctb], Kentaro Matsuura [ctb]

occumb_1.3.0.tar.gz
occumb_1.3.0.zip(r-4.7)occumb_1.3.0.zip(r-4.6)occumb_1.3.0.zip(r-4.5)
occumb_1.3.0.tgz(r-4.6-any)occumb_1.3.0.tgz(r-4.5-any)
occumb_1.3.0.tar.gz(r-4.7-any)occumb_1.3.0.tar.gz(r-4.6-any)
occumb_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
occumb/json (API)

# Install 'occumb' in R:
install.packages('occumb', repos = c('https://fukayak.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fukayak/occumb/issues

Pkgdown/docs site:https://fukayak.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • fish - Fish eDNA metabarcoding dataset
  • fish_raw - Fish eDNA metabarcoding dataset

On CRAN:

Conda:

jagscpp

6.29 score 3 stars 29 scripts 549 downloads 12 exports 12 dependencies

Last updated from:25359166c5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK171
source / vignettesOK198
linux-release-x86_64OK151
macos-release-arm64OK179
macos-oldrel-arm64OK221
windows-develOK110
windows-releaseOK99
windows-oldrelOK106
wasm-releaseOK162

Exports:eval_util_Leval_util_Rget_post_samplesget_post_summarygoflist_cond_Llist_cond_RoccumboccumbDataplotpredictsummary

Dependencies:backportscheckmatecodacrayonevaluatehighrjagsUIknitrlatticerjagsxfunyaml

Introduction to occumb
Prepare dataset | Fit models | Check posterior samples | Predict parameter values | Assess goodness-of-fit | Analyze study design
Rendered fromoccumb.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2023-07-20

Options for MCMC engines in occumb()
Benchmarks | Fish dataset | Aquatic insects dataset | Conclusion
Rendered frommcmc_engine_options.Rmdusingknitr::rmarkdown

Last update: 2026-04-03
Started: 2026-04-03

Model specification in occumb()
Modeling the sequential sampling process of eDNA metabarcoding | Covariate modeling of psi, theta, and phi | Prior distributions | After all, which are the relevant parameters?
Rendered frommodel_specification.Rmdusingknitr::rmarkdown

Last update: 2025-07-16
Started: 2023-07-20